scripts/Overlap.rerunAWS.sh
#!/bin/bash
humanRef=$1
File=$2
FinalCoverage=$3
NameStub=$4.V2
HashList=$5
HashSize=$6
Threads=$7
 
SampleJhash=$8
ParentsJhash=$9

humanRefBwa=${10}
refHash=${11}
MaxCov=100000
echo " you gave
File=$2
FinalCoverage=$3
NameStub=$4.V2
HashList=$5
HashSize=$6
Threads=$7
"

echo "final coveage is $FinalCoverage"


echo "RUNNING THIS ONE"
echo "@@@@@@@@@@@@@__IN_OVERLAP__@@@@@@@@@@@@@@@"
echo "human ref in Overlap is $humanRef"
echo "bwa human ref in Overlap is $humanRefBwa"
echo "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
mkdir ./TempOverlap/
mkdir ./Intermediates/
echo "Overlaping $File"

CDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"


RDIR=$CDIR/../

OverlapHash=$RDIR/bin/Overlap
OverlapRebion2=$RDIR/bin/OverlapRegion
ReplaceQwithDinFASTQD=$RDIR/bin/ReplaceQwithDinFASTQD
ConvertFASTqD=$RDIR/bin/ConvertFASTqD.to.FASTQ
AnnotateOverlap=$RDIR/bin/AnnotateOverlap
bwa=$RDIR/bin/externals/bwa/src/bwa_project/bwa
RUFUSinterpret=$RDIR/bin/RUFUS.interpret
CheckHash=$RDIR/scripts/CheckJellyHashList.sh
OverlapSam=$RDIR/bin/OverlapSam
JellyFish=$RDIR/bin/externals/jellyfish/src/jellyfish_project/bin/jellyfish
MOBList=$RDIR/resources/primate_non-LTR_Retrotransposon.fasta

#if [ -s $NameStub.overlap.hashcount.fastq ]
#then 
#	echo "Skipping Overlap"
#else


if [ -s ./$File.bam ] 
then 
	echo "skipping align"
else
	$bwa mem -t $Threads $humanRefBwa "$File" | samtools sort -T $File -O bam - > $File.bam
	samtools index $File.bam 
fi

if [ -s ./TempOverlap/$NameStub.sam.fastqd ]  
then 
	echo "skipping sam assemble"
else
     
	$OverlapSam <( samtools view  -F 3328 $File.bam | awk '$9 > 100 || $9 < -100 || $9==0' ) .95 20 1 ./TempOverlap/$NameStub.sam $NameStub 1 $HashList $Threads
	#$OverlapSam <( samtools view  -F 3328 $File.bam ) .95 20 1 ./TempOverlap/$NameStub.sam $NameStub 1 $HashList $Threads
fi
if [ -s ./TempOverlap/$NameStub.1.fastqd ]
then 	
	echo "skipping first overlap"
else
	time $OverlapHash ./TempOverlap/$NameStub.sam.fastqd .98 50 1 FP 20 1 ./TempOverlap/$NameStub.1 0 $Threads #> $File.overlap.out
fi 
if [ -s ./TempOverlap/$NameStub.2.fastqd ]
then 
	echo "skipping second overlap"
else
	time $OverlapHash ./TempOverlap/$NameStub.1.fastqd .98 50 2 FP 20 1 ./TempOverlap/$NameStub.2 1 $Threads #>>  $File.overlap.out
fi
if [ -s ./TempOverlap/$NameStub.3.fastqd ]
then
        echo "skipping second overlap"
else
        time $OverlapHash ./TempOverlap/$NameStub.2.fastqd .98 25 2 $NameStub 20 1 ./TempOverlap/$NameStub.3 1 $Threads #>>  $File.overlap.out
fi
if [ -s ./TempOverlap/$NameStub.4.fastqd ]
then
        echo "skipping second overlap"
else
        time $OverlapRebion2 ./TempOverlap/$NameStub.3.fastqd .98 25 $FinalCoverage  ./TempOverlap/$NameStub.4 $NameStub 1 $Threads > /dev/null
	#time $OverlapHash ./TempOverlap/$NameStub.3.fastqd .98 25 $FinalCoverage $NameStub 15 1 ./TempOverlap/$NameStub.4 1 $Threads #>>  $File.overlap.out
fi
if [ -s ./$NameStub.overlap.hashcount.fastq ]
then 
	echo "skipping final overlap work"
else

	$ReplaceQwithDinFASTQD ./TempOverlap/$NameStub.4.fastqd > ./$NameStub.overlap.fastqd
	$ConvertFASTqD ./$NameStub.overlap.fastqd > ./$NameStub.overlap.fastq

	echo "$AnnotateOverlap $HashList ./$NameStub.overlap.fastq TempOverlap/$NameStub.overlap.asembly.hash.fastq > ./$NameStub.overlap.hashcount.fastq"              
	      $AnnotateOverlap $HashList ./$NameStub.overlap.fastq TempOverlap/$NameStub.overlap.asembly.hash.fastq > ./$NameStub.overlap.hashcount.fastq
fi


if [ -s ./$NameStub.overlap.hashcount.fastq.bam ]
then 
	echo "skipping contig alignment" 
else
        $bwa mem -t $Threads -Y -E 0,0 -O 6,6  -d 500 -w 500 -L 2,2 $humanRefBwa ./$NameStub.overlap.hashcount.fastq | samtools sort -T $File -O bam - > ./$NameStub.overlap.hashcount.fastq.bam
	samtools index ./$NameStub.overlap.hashcount.fastq.bam
fi

if [ -s ./TempOverlap/$NameStub.overlap.hashcount.fastq.MOB.sam ]
then
	echo "skipping MOB alignemnt check "
else 
	$bwa mem -t $Threads -Y -E 0,0 -O 6,6  -d 500 -w 500 -L 0,0 $MOBList ./$NameStub.overlap.hashcount.fastq | samtools sort -T $File -O sam - > ./TempOverlap/$NameStub.overlap.hashcount.fastq.MOB.sam
fi 


#############################################################################################################

parentCRString=""
c="-c"
cr="-cR"
space=" "


######################## BUILDING UP parent c and cR string ##############################
for parent in $ParentsJhash;
do
    parentCRString="$parentCRString -c ./Intermediates/$NameStub.overlap.asembly.hash.fastq.$parent -cR ./Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.$parent "
done

#echo "final parent String is  $parentCRString"
##########################################################################################

mkfifo check 
samtools index ./$NameStub.overlap.hashcount.fastq.bam

echo "$RUFUSinterpret -mob ./TempOverlap/$NameStub.overlap.hashcount.fastq.MOB.sam  -mod Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -mQ 8 -r $humanRef -hf $HashList -o  ./$NameStub.overlap.hashcount.fastq.bam -m 1000000 $(echo $parentCRString) -sR Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample -s Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -e ./Intermediates/$NameStub.ref.RepRefHash "

echo ""
echo "" 
echo ""
echo "$RUFUSinterpret -mob ./TempOverlap/$NameStub.overlap.hashcount.fastq.MOB.sam -mod Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -mQ 8 -r $humanRef -hf $HashList -o  ./$NameStub.overlap.hashcount.fastq.bam -m 1000 $(echo $parentCRString) -sR Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample -s Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -e ./Intermediates/$NameStub.ref.RepRefHash"
samtools view ./$NameStub.overlap.hashcount.fastq.bam | $RUFUSinterpret -mob ./TempOverlap/$NameStub.overlap.hashcount.fastq.MOB.sam -mod Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -mQ 8 -r $humanRef -hf $HashList -o  ./$NameStub.overlap.hashcount.fastq.bam -m 1000 $(echo $parentCRString) -sR Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample -s Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -e ./Intermediates/$NameStub.ref.RepRefHash 


